grepq: A Rust application that quickly filters FASTQ files by matching sequences to a set of regular expressions

Abstract

Regular expressions (regex) (Kleene 1951) have been an important tool for finding patterns in biological codes for decades (Hodgman 2000 and citations therein), and unlike fuzzy-finding approaches, do not result in approximate matches. The performance of regular expressions can be slow, however, especially when searching for matching patterns in large files. grepq is a Rust application that quickly filters FASTQ files by matching sequences to a set of regular expressions. grepq is designed with a focus on performance and scalability, is easy to install and easy to use, enabling users to quickly filter large FASTQ files, to enumerate named and unnamed variants, to update the order in which patterns are matched against sequences through in-built tune and summarise commands, and optionally, to output a SQLite file for further sequence analysis. grepq is open-source and available on GitHub and Crates.io.